Which is the most preferred way for distributing an enterprise iOS application with-in the organization? Since this is an enterprise application, user has to be authenticated before they download? Which is the commonly practiced approach for this? (If this question doesn't belong to this area, please suggest the correct one)
If you are a registered developer with an enterprise account and are making apps for in-house distribution, TestFlight works with those too. TestFlight fully supports enterprise apps and it works much like ad hoc apps for distribution. Just upload an application signed with an enterprise provisioning profile and distribute to your team and only approved members of your team will have access to the application for installation.
For Production release you can go for any one of the following way
Enterprise in house apps
.
Here is the example for Wireless Distribution of enterprise apps.Regarding the security part you have to make sure that your webserver link is protected with user name and password such as linking with LDAP or custom code to validate.